# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 23:19:00 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-[2-(4-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CCC2=C(NC(=O)NC2=O)C(O)=O)cc1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VRO  VRO  '5-[2-(4-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  35  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VRO
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VRO  OAB  O  O     0  -0.396   1.0287   2.5455  -0.2183
 VRO  CAO  C  C     0   0.521   2.1492   2.2111   0.0546
 VRO  OAE  O  OH1   0  -0.590   3.1344   3.0431   0.3395
 VRO  CAR  C  CR6   0   0.282   2.6145   0.7870   0.0976
 VRO  NAL  N  NR16  0  -0.732   3.9590   0.6121  -0.1167
 VRO  CAT  C  CR6   0   0.670   4.5791  -0.6019  -0.1487
 VRO  OAC  O  O     0  -0.473   5.7669  -0.7385  -0.3530
 VRO  NAM  N  NR16  0  -0.716   3.7299  -1.6549   0.0702
 VRO  CAU  C  CR6   0   0.586   2.3737  -1.5979   0.3088
 VRO  OAD  O  O     0  -0.441   1.7383  -2.6187   0.4869
 VRO  CAS  C  CR6   0  -0.119   1.7847  -0.2548   0.3250
 VRO  CAK  C  CH2   0  -0.500   0.3101  -0.1796   0.5753
 VRO  CAJ  C  CH2   0  -0.501  -0.5067  -0.3775  -0.7119
 VRO  CAP  C  CR6   0   0.103  -1.9816  -0.2365  -0.4646
 VRO  CAF  C  CR16  0  -0.287  -2.5536   1.0246  -0.2833
 VRO  CAH  C  CR16  0  -0.328  -3.9036   1.1756  -0.0316
 VRO  CAQ  C  CR6   0   0.365  -4.7339   0.0545   0.0462
 VRO  OAN  O  O2    0  -0.473  -6.0393   0.2934   0.2865
 VRO  CAA  C  CH3   0  -0.436  -6.9296  -0.8028   0.3179
 VRO  CAI  C  CR16  0  -0.369  -4.1819  -1.2107  -0.1278
 VRO  CAG  C  CR16  0  -0.305  -2.8185  -1.3397  -0.3784
 VRO  H1   H  HOH1  0   0.504   2.8384   3.9643   0.2680
 VRO  H2   H  HNR6  0   0.431   4.1490  -2.5768   0.0457
 VRO  H4   H  HCH2  0   0.260   0.0417  -0.9603   1.2888
 VRO  H5   H  HCH2  0   0.264   0.0414   0.7676   1.0367
 VRO  H6   H  HCH2  0   0.251  -0.1825   0.3546  -1.4540
 VRO  H7   H  HCH2  0   0.249  -0.2929  -1.3640  -1.1271
 VRO  H8   H  HCR6  0   0.249  -1.9280   1.9078  -0.3462
 VRO  H9   H  HCR6  0   0.258  -4.3278   2.1634   0.1016
 VRO  H10  H  HCH3  0   0.226  -6.6940  -1.5017   1.1253
 VRO  H11  H  HCH3  0   0.259  -7.9212  -0.3921   0.4910
 VRO  H12  H  HCH3  0   0.226  -6.9371  -1.3501  -0.6287
 VRO  H13  H  HCR6  0   0.274  -4.7900  -2.1037  -0.0753
 VRO  H14  H  HCR6  0   0.248  -2.4098  -2.3342  -0.5164
 VRO  H15  H  HNR6  0   0.439   4.5472   1.4165  -0.2835

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VRO  CAA  OAN  single    1.413  0.020  1.413
 VRO  CAI  CAG  aromatic  1.392  0.020  1.392
 VRO  CAI  CAQ  aromatic  1.391  0.020  1.391
 VRO  CAG  CAP  aromatic  1.387  0.020  1.387
 VRO  OAN  CAQ  single    1.349  0.020  1.349
 VRO  CAQ  CAH  aromatic  1.397  0.020  1.397
 VRO  CAP  CAJ  single    1.502  0.020  1.502
 VRO  CAP  CAF  aromatic  1.397  0.020  1.397
 VRO  CAJ  CAK  single    1.537  0.020  1.537
 VRO  CAF  CAH  aromatic  1.382  0.020  1.382
 VRO  CAK  CAS  single    1.498  0.020  1.498
 VRO  OAD  CAU  double    1.216  0.020  1.216
 VRO  CAS  CAU  single    1.467  0.020  1.467
 VRO  CAS  CAR  double    1.351  0.020  1.351
 VRO  CAU  NAM  single    1.378  0.020  1.378
 VRO  CAR  CAO  single    1.499  0.020  1.499
 VRO  CAR  NAL  single    1.373  0.020  1.373
 VRO  OAB  CAO  double    1.201  0.020  1.201
 VRO  NAM  CAT  single    1.370  0.020  1.370
 VRO  CAO  OAE  single    1.321  0.020  1.321
 VRO  NAL  CAT  single    1.364  0.020  1.364
 VRO  CAT  OAC  double    1.213  0.020  1.213
 VRO  OAE  H1   single    0.850  0.020  0.980
 VRO  NAM  H2   single    0.860  0.020  1.020
 VRO  CAK  H4   single    0.970  0.020  1.090
 VRO  CAK  H5   single    0.970  0.020  1.090
 VRO  CAJ  H6   single    0.970  0.020  1.090
 VRO  CAJ  H7   single    0.970  0.020  1.090
 VRO  CAF  H8   single    0.930  0.020  1.080
 VRO  CAH  H9   single    0.930  0.020  1.080
 VRO  CAA  H10  single    0.970  0.020  1.090
 VRO  CAA  H11  single    0.970  0.020  1.090
 VRO  CAA  H12  single    0.970  0.020  1.090
 VRO  CAI  H13  single    0.930  0.020  1.080
 VRO  CAG  H14  single    0.930  0.020  1.080
 VRO  NAL  H15  single    0.860  0.020  1.020

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VRO  CAR  CAO  OAE  111.15  3.000
 VRO  OAE  CAO  OAB  124.73  3.000
 VRO  CAR  CAO  OAB  124.11  3.000
 VRO  H1   OAE  CAO  110.77  3.000
 VRO  CAS  CAR  NAL  121.98  3.000
 VRO  NAL  CAR  CAO  114.87  3.000
 VRO  CAS  CAR  CAO  123.15  3.000
 VRO  H15  NAL  CAT  116.12  3.000
 VRO  H15  NAL  CAR  119.64  3.000
 VRO  CAT  NAL  CAR  124.23  3.000
 VRO  NAM  CAT  OAC  123.18  3.000
 VRO  OAC  CAT  NAL  123.33  3.000
 VRO  NAM  CAT  NAL  113.49  3.000
 VRO  H2   NAM  CAU  116.68  3.000
 VRO  H2   NAM  CAT  116.05  3.000
 VRO  CAU  NAM  CAT  127.27  3.000
 VRO  CAS  CAU  OAD  123.88  3.000
 VRO  CAS  CAU  NAM  115.79  3.000
 VRO  OAD  CAU  NAM  120.33  3.000
 VRO  CAK  CAS  CAU  116.31  3.000
 VRO  CAU  CAS  CAR  117.23  3.000
 VRO  CAK  CAS  CAR  126.45  3.000
 VRO  H5   CAK  H4   106.56  3.000
 VRO  H5   CAK  CAJ  109.64  3.000
 VRO  H4   CAK  CAJ  108.95  3.000
 VRO  H5   CAK  CAS  110.98  3.000
 VRO  H4   CAK  CAS  108.39  3.000
 VRO  CAJ  CAK  CAS  112.13  3.000
 VRO  H7   CAJ  H6   106.81  3.000
 VRO  H7   CAJ  CAP  109.87  3.000
 VRO  H6   CAJ  CAP  109.91  3.000
 VRO  H7   CAJ  CAK  109.32  3.000
 VRO  H6   CAJ  CAK  108.97  3.000
 VRO  CAP  CAJ  CAK  111.83  3.000
 VRO  CAG  CAP  CAF  117.57  3.000
 VRO  CAF  CAP  CAJ  120.55  3.000
 VRO  CAG  CAP  CAJ  121.86  3.000
 VRO  H8   CAF  CAH  119.04  3.000
 VRO  H8   CAF  CAP  119.45  3.000
 VRO  CAH  CAF  CAP  121.51  3.000
 VRO  H9   CAH  CAQ  119.48  3.000
 VRO  H9   CAH  CAF  120.31  3.000
 VRO  CAQ  CAH  CAF  120.20  3.000
 VRO  CAI  CAQ  OAN  124.57  3.000
 VRO  OAN  CAQ  CAH  116.29  3.000
 VRO  CAI  CAQ  CAH  119.14  3.000
 VRO  CAA  OAN  CAQ  118.46  3.000
 VRO  H12  CAA  H11  108.70  3.000
 VRO  H12  CAA  H10  108.71  3.000
 VRO  H11  CAA  H10  108.68  3.000
 VRO  H12  CAA  OAN  111.94  3.000
 VRO  H11  CAA  OAN  106.58  3.000
 VRO  H10  CAA  OAN  112.13  3.000
 VRO  H13  CAI  CAG  118.86  3.000
 VRO  H13  CAI  CAQ  121.45  3.000
 VRO  CAG  CAI  CAQ  119.69  3.000
 VRO  H14  CAG  CAI  118.50  3.000
 VRO  H14  CAG  CAP  119.62  3.000
 VRO  CAI  CAG  CAP  121.88  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VRO  CONST_01  CAQ  CAI  CAG  CAP     0.00   0.0  0
 VRO  CONST_02  CAQ  CAH  CAF  CAP     0.00   0.0  0
 VRO  CONST_03  CAI  CAG  CAP  CAF     0.00   0.0  0
 VRO  CONST_04  CAI  CAQ  CAH  CAF     0.00   0.0  0
 VRO  CONST_05  CAG  CAI  CAQ  CAH     0.00   0.0  0
 VRO  CONST_06  CAG  CAP  CAF  CAH     0.00   0.0  0
 VRO  CONST_07  NAM  CAT  NAL  CAR     0.00   0.0  0
 VRO  CONST_08  CAU  NAM  CAT  NAL     0.00   0.0  0
 VRO  CONST_09  CAS  CAU  NAM  CAT     0.00   0.0  0
 VRO  CONST_10  CAI  CAG  CAP  CAJ   180.00   0.0  0
 VRO  CONST_11  CAH  CAF  CAP  CAJ   180.00   0.0  0
 VRO  CONST_12  OAN  CAQ  CAH  CAF   180.00   0.0  0
 VRO  CONST_13  CAG  CAI  CAQ  OAN   180.00   0.0  0
 VRO  CONST_14  OAC  CAT  NAL  CAR   180.00   0.0  0
 VRO  CONST_15  OAD  CAU  NAM  CAT   180.00   0.0  0
 VRO  CONST_16  CAU  NAM  CAT  OAC   180.00   0.0  0
 VRO  CONST_17  H13  CAI  CAG  CAP   180.00   0.0  0
 VRO  CONST_18  H9   CAH  CAF  CAP   180.00   0.0  0
 VRO  CONST_19  H14  CAG  CAP  CAF   180.00   0.0  0
 VRO  CONST_20  H8   CAF  CAH  CAQ   180.00   0.0  0
 VRO  CONST_21  H2   NAM  CAT  NAL   180.00   0.0  0
 VRO  CONST_22  H15  NAL  CAT  NAM   180.00   0.0  0
 VRO  CONST_23  H1   OAE  CAO  CAR   180.00   0.0  0
 VRO  Var_01    CAS  CAR  CAO  OAB   -25.29  30.0  2
 VRO  Var_02    CAJ  CAK  CAS  CAR    94.68  30.0  2
 VRO  Var_03    CAP  CAJ  CAK  CAS  -177.32  30.0  1
 VRO  Var_04    CAG  CAP  CAJ  CAK  -102.80  30.0  2
 VRO  Var_05    CAI  CAQ  OAN  CAA    -2.46  30.0  2
 VRO  Var_06    H10  CAA  OAN  CAQ    63.01  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VRO  plan-1  CAO  0.020
 VRO  plan-1  CAR  0.020
 VRO  plan-1  NAL  0.020
 VRO  plan-1  CAT  0.020
 VRO  plan-1  OAC  0.020
 VRO  plan-1  NAM  0.020
 VRO  plan-1  CAU  0.020
 VRO  plan-1  OAD  0.020
 VRO  plan-1  CAS  0.020
 VRO  plan-1  CAK  0.020
 VRO  plan-1  H2   0.020
 VRO  plan-1  H15  0.020
 VRO  plan-2  CAJ  0.020
 VRO  plan-2  CAP  0.020
 VRO  plan-2  CAF  0.020
 VRO  plan-2  CAH  0.020
 VRO  plan-2  CAQ  0.020
 VRO  plan-2  OAN  0.020
 VRO  plan-2  CAI  0.020
 VRO  plan-2  CAG  0.020
 VRO  plan-2  H8   0.020
 VRO  plan-2  H9   0.020
 VRO  plan-2  H13  0.020
 VRO  plan-2  H14  0.020
 VRO  plan-3  OAB  0.020
 VRO  plan-3  CAO  0.020
 VRO  plan-3  OAE  0.020
 VRO  plan-3  CAR  0.020
 VRO  plan-3  H1   0.020

